The David Miranda story has proved rather confusing – and not just because the constant use of "Miranda" to refer to the case conjures up images of Miranda Hart prat-falling her way through airport security.

As with any Glenn Greenwald scoop, the picture is not as simple as it was first presented.

Rather than being stopped simply for being the partner of a journalist, it has now emerged that Mr Miranda was travelling as part of a Guardian investigation, assisting Greenwald's research and allegedly carrying some of the leaked Snowden information about his person. Nor was he refused access to a lawyer – he rejected the one offered to him.

To stop a journalist's family is crude intimidation of the grubbiest kind, but David Miranda was much more than simply a family member, he was acting as a journalist himself.

Of course, intimidating journalists is almost as grubby as intimidating their families – but the distinction is enough to suggest Greenwald's version of events was partial at best.

Similary, we cannot be certain that the Government's account of the processes and decisions that led to Mr Miranda's encounter with the Terrorism Act is necessarily true or complete.

As we've seen all too often in the past, once the security services get mixed up in political communications things have a nasty habit of being forgotten, or "mis-spoken" as Hillary Clinton would put it.

So, unable to fully trust either story, we now have to deal with the news that "senior Whitehall figures" pressured the Guardian into allowing GCHQ officials to destroy computers at their office, supposedly in order to wipe the Snowden data they held.

Destroying a couple of computers in an age when things can be copied and sent around the world at the click of a button – and when others are couriering copies by airplane – is a bizarre decision. GCHQ may not be perfect but they surely know that taking an angle grinder to a Macbook is of little practical use (though it is a neat analogy for what the newspaper-buying public is doing to the Guardian, as it happens).

Evidently we are yet to discover the full story – indeed, we may never know exactly what went on and why – but there are a few initial conclusions we can draw:

State influence on the media is not a pretty sight

While the Guardian was more than happy to support state control of the media when they thought it meant Leveson kicking Rupert Murdoch, it turns out they don't like it so much when it applies to them.

The media has an essential role in any democracy to scrutinise those in power, including the security services. We should be deeply uncomfortable about the idea those services have apparently used anti-terror powers to try to deter journalists from carrying out that role – whether we agree with the journalists' politics or not.

The Terrorism Act is too loosely worded…

I have been stopped, albeit briefly, under Section 44 of the Terrorism Act for protesting outside a Labour conference (against ID cards, appropriately enough), and I can confirm that its logic is troubling.

We are used to the idea that the police only get to exercise their powers when they have some reason to suspect wrongdoing – be it evidence, intelligence or the observations of an officer on the spot. It is out of keeping with the traditions of British law (as well as a colossal waste of police time) for officers to go stopping people with no grounds for suspicion at all.

In Opposition, the Conservatives rightly criticised the Blair government for its abuse of freedom in the name of security, and for its failure to understand our legal traditions. We should be proud of following through on those criticisms by destroying the ID card scheme, for example – but it is clear there is plenty work left undone.

…and its use is too lightly supervised

Section 7 of the Terrorism Act has never previously received much attention, but now that it has several inconsistencies have come to light. While the Act states that officers need no grounds for suspicion to use its powers, the Home Office guidelines state that it should not be used "arbitrarily". This makes little sense – what can be more arbitrary than the police detaining someone for questioning and investigation about their links to terrorism with no reason to suspect the person in question of any terrorist activity whatsoever?

As Louise Mensch argues, it may well be that there were legitimate security grounds for stopping David Miranda. The documents he was allegedly handling relate to American and British security services. The Snowden files were certainly stolen. Even if he and Greenwald had no malicious intent, their computers are likely less well protected from Chinese hackers than GCHQ's or the CIA's.

But, as Big Brother Watch point out, none of those issues constitutes terrorism. Unsurprisingly, the Terrorism Act is meant to be used on terrorists, not troublesome journalists.

Why not use another law relating to official secrets, or the transporting of information which poses a threat to national security or the lives of any agents who might be exposed? For that matter, why did they wait until he was passing through Heathrow rather than use the European Arrest Warrant to get him brought in custody from Germany?

The answer is that those alternatives would have required evidence and due process – neither of which, it seems, the security services wished to be troubled with.

As Conservatives, we should be concerned with preserving the security of our nation. But we should also remember that freedom of the press and the rule of law are essential elements of the nation we seek to defend. Balancing those competing concerns, often to the annoyance of all involved, is a difficult task but it is also an essential one.

Conservatism means dealing with these issues as they are in the real world, not just steamrollering one side in order to look tough – that was Tony Blair's approach, and it created this mess in the first place.

More information is certain to come to light in this story – claim and counter-claim, assertion and rebuttal. Things will probably get a lot murkier before they even start to become any more clear.